Q6LYM1 (DNLI_METMP) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA ligase
EC=6.5.1.1

Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]

Gene names

Name:	lig
Ordered Locus Names:	MMP0970

Organism

Methanococcus maripaludis (strain S2 / LL) [Complete proteome] [HAMAP]

Taxonomic identifier

267377 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanococcaceae › Methanococcus › Methanococcus maripaludis

Protein attributes

Sequence length	573 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair By similarity. HAMAP-Rule MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_00407
Cofactor	Divalent metal cations By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Ligand	ATP-binding Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: HAMAP DNA replication Inferred from electronic annotation. Source: HAMAP cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 573	573	DNA ligase HAMAP-Rule MF_00407		PRO_0000059607
Sites
	Active site	252	1	N6-AMP-lysine intermediate By similarity
	Binding site	250	1	ATP By similarity
	Binding site	257	1	ATP By similarity
	Binding site	272	1	ATP By similarity
	Binding site	301	1	ATP By similarity
	Binding site	342	1	ATP By similarity
	Binding site	432	1	ATP By similarity
	Binding site	438	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q6LYM1 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 0E7E33F72388095B	FASTA	573	65,752
	10 20 30 40 50 60 MLFSDFCKIL DKIEKTTKRL EKTDYFVELI DFIKTSEKPE NLKQVSQITI GRVFAEFENK 70 80 90 100 110 120 EIGIGPNLLL EAVKTTGIPE KDLKSKIKET GDIGTAVENL SSNIKQVSLF SQALTLEEVY 130 140 150 160 170 180 STLKKLSEIE GNSSQKKKTR IISNLLILAD PVESRYISRL ILEDMRIGMN IPTILASFSN 190 200 210 220 230 240 YFNVNKESVE KIYAVTNDIG LLGEKLISGS DIENDPELKL KVFRPIKPML AQLTPSIEDA 250 260 270 280 290 300 MIETKMPQFE TKYDGARVQV HKSNGDVKIY SRRLENITNS VPELVEEIKK LDIDNIILEG 310 320 330 340 350 360 ECVAMDLDSG KPRPFQDILR RFRRKYNIDK MAEKIALRIY FFDVLYYNRG LIDTPLKTRR 370 380 390 400 410 420 EILEKLFGTN NWDSELEKIK KEIFSSKMLF SSFKLNSGDP NLVKEFFNWS LSIGHEGIMI 430 440 450 460 470 480 KNPDAPYTPG SRVKTMYKVK PTLENLDVVV TRAKIGMGKR KDWYGSYELS VKDNDGNLHV 490 500 510 520 530 540 IGNVGSGLTE DDLEKLTKIV NEIKIEDLGE EVILEPKIVL EVTYEEIQTS EKYEMGYALR 550 560 570 FPRVVQIRED KSINDINTLD DVKKIYEIER NRK

References

[1]

"Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis." Hendrickson E.L., Kaul R., Zhou Y., Bovee D., Chapman P., Chung J., Conway de Macario E., Dodsworth J.A., Gillett W., Graham D.E., Hackett M., Haydock A.K., Kang A., Land M.L., Levy R., Lie T.J., Major T.A., Moore B.C. , Porat I., Palmeiri A., Rouse G., Saenphimmachak C., Soell D., Van Dien S., Wang T., Whitman W.B., Xia Q., Zhang Y., Larimer F.W., Olson M.V., Leigh J.A. J. Bacteriol. 186:6956-6969(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: S2 / LL.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BX950229 Genomic DNA. Translation: CAF30526.1.
RefSeq	NP_988090.1. NC_005791.1.
3D structure databases
ProteinModelPortal	Q6LYM1.
ModBase	Search...
Protein-protein interaction databases
STRING	267377.MMP0970.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	CAF30526; CAF30526; MMP0970.
GeneID	2761378.
KEGG	mmp:MMP0970.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1793.
HOGENOM	HOG000036008.
KO	K10747.
OMA	ARVQVHK.
ProtClustDB	CLSK876100.
Enzyme and pathway databases
BioCyc	MMAR267377:GJ77-1000-MONOMER.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
HAMAP	MF_00407. DNA_ligase.
InterPro	IPR022865. DNA_ligae_ATP-dep_bac/arc. IPR000977. DNA_ligase_ATP-dep. IPR012309. DNA_ligase_ATP-dep_C. IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR012308. DNA_ligase_ATP-dep_N. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI_METMP

Accession

Primary (citable) accession number: Q6LYM1

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 21, 2004
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 61 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program